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HicAggR

Set of 3D genomic interaction analysis tools

https://github.com/cuvierlab/hicaggr

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary

Keywords

r r-package
Last synced: 7 months ago · JSON representation

Repository

Set of 3D genomic interaction analysis tools

Basic Info
  • Host: GitHub
  • Owner: CuvierLab
  • License: other
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 21.6 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Topics
r r-package
Created over 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# HicAggR 


[![R-CMD-check](https://github.com/CuvierLab/HicAggR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/CuvierLab/HicAggR/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/CuvierLab/HicAggR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/CuvierLab/HicAggR?branch=master)


This package provides a set of functions useful in the analysis of 3D genomic interactions.
It includes the import of standard HiC data formats into R and HiC normalisation procedures.
The main objective of this package is to improve the visualization and quantification of the analysis of HiC contacts through aggregation.




## Installation

Development version is avalaible from [GitHub](https://github.com/):

``` r
remotes::install_github("CuvierLab/HicAggR")
```

## Documentation  

[HicAggR](https://cuvierlab.github.io/HicAggR/)

Owner

  • Name: CuvierLab
  • Login: CuvierLab
  • Kind: organization

GitHub Events

Total
  • Issues event: 1
  • Watch event: 1
Last Year
  • Issues event: 1
  • Watch event: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 1
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 21 hours
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 21 hours
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • PengfeiInTuebingen (1)
Pull Request Authors
  • RobTesf (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 1,592 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
bioconductor.org: HicAggR

Set of 3D genomic interaction analysis tools

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 1,592 Total
Rankings
Dependent repos count: 0.0%
Average: 15.6%
Dependent packages count: 31.3%
Maintainers (1)
olivier.cuvier@univ-tlse3.fr
Last synced: over 1 year ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action 4.1.4 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 4.2.0 depends
  • BiocGenerics * imports
  • BiocParallel * imports
  • GenomeInfoDb * imports
  • GenomicRanges * imports
  • IRanges * imports
  • InteractionSet * imports
  • Matrix * imports
  • S4Vectors * imports
  • data.table * imports
  • dplyr * imports
  • ggplot2 * imports
  • grDevices * imports
  • gridExtra * imports
  • methods * imports
  • reshape * imports
  • rhdf5 * imports
  • rlang * imports
  • rtracklayer * imports
  • stats * imports
  • strawr * imports
  • stringr * imports
  • tibble * imports
  • tidyr * imports
  • utils * imports
  • covr * suggests
  • kableExtra >= 1.3.4 suggests
  • knitr >= 1.45 suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests